Current methods for routine and large scale analysis of target polynucleotides require the preparation of tens to thousands to millions of individual target samples, which are processed and analyzed in individual reaction vessels. Therefore, labor, materials, and equipment are a significant cost of target polynucleotide analysis regardless of the methodology employed.
To increase the number of target polynucleotides that can be discretely and simultaneously analyzed in a reaction vessel, the present disclosure provides compositions and methods for making reaction mixtures having individual reaction compartments. The reaction compartments are suitable for processing and analyzing one or more target polynucleotides by various methods.